#
# Generated Mon Jun 27 10:13:43 2011 by generateDS.py version 2.5b.
#

import sys
import getopt
import re as re_

etree_ = None
Verbose_import_ = False
(   XMLParser_import_none, XMLParser_import_lxml,
    XMLParser_import_elementtree
    ) = list(range(3))
XMLParser_import_library = None
try:
    # lxml
    from lxml import etree as etree_
    XMLParser_import_library = XMLParser_import_lxml
    if Verbose_import_:
        print("running with lxml.etree")
except ImportError:
    try:
        # cElementTree from Python 2.5+
        import xml.etree.cElementTree as etree_
        XMLParser_import_library = XMLParser_import_elementtree
        if Verbose_import_:
            print("running with cElementTree on Python 2.5+")
    except ImportError:
        try:
            # ElementTree from Python 2.5+
            import xml.etree.ElementTree as etree_
            XMLParser_import_library = XMLParser_import_elementtree
            if Verbose_import_:
                print("running with ElementTree on Python 2.5+")
        except ImportError:
            try:
                # normal cElementTree install
                import cElementTree as etree_
                XMLParser_import_library = XMLParser_import_elementtree
                if Verbose_import_:
                    print("running with cElementTree")
            except ImportError:
                try:
                    # normal ElementTree install
                    import elementtree.ElementTree as etree_
                    XMLParser_import_library = XMLParser_import_elementtree
                    if Verbose_import_:
                        print("running with ElementTree")
                except ImportError:
                    raise ImportError("Failed to import ElementTree from any known place")

def parsexml_(*args, **kwargs):
    if (XMLParser_import_library == XMLParser_import_lxml and
        'parser' not in kwargs):
        # Use the lxml ElementTree compatible parser so that, e.g.,
        #   we ignore comments.
        kwargs['parser'] = etree_.ETCompatXMLParser()
    doc = etree_.parse(*args, **kwargs)
    return doc

#
# User methods
#
# Calls to the methods in these classes are generated by generateDS.py.
# You can replace these methods by re-implementing the following class
#   in a module named generatedssuper.py.

try:
    from generatedssuper import GeneratedsSuper
except ImportError as exp:

    class GeneratedsSuper(object):
        def gds_format_string(self, input_data, input_name=''):
            return input_data
        def gds_validate_string(self, input_data, node, input_name=''):
            return input_data
        def gds_format_integer(self, input_data, input_name=''):
            return '%d' % input_data
        def gds_validate_integer(self, input_data, node, input_name=''):
            return input_data
        def gds_format_integer_list(self, input_data, input_name=''):
            return '%s' % input_data
        def gds_validate_integer_list(self, input_data, node, input_name=''):
            values = input_data.split()
            for value in values:
                try:
                    fvalue = float(value)
                except (TypeError, ValueError) as exp:
                    raise_parse_error(node, 'Requires sequence of integers')
            return input_data
        def gds_format_float(self, input_data, input_name=''):
            return '%f' % input_data
        def gds_validate_float(self, input_data, node, input_name=''):
            return input_data
        def gds_format_float_list(self, input_data, input_name=''):
            return '%s' % input_data
        def gds_validate_float_list(self, input_data, node, input_name=''):
            values = input_data.split()
            for value in values:
                try:
                    fvalue = float(value)
                except (TypeError, ValueError) as exp:
                    raise_parse_error(node, 'Requires sequence of floats')
            return input_data
        def gds_format_double(self, input_data, input_name=''):
            return '%e' % input_data
        def gds_validate_double(self, input_data, node, input_name=''):
            return input_data
        def gds_format_double_list(self, input_data, input_name=''):
            return '%s' % input_data
        def gds_validate_double_list(self, input_data, node, input_name=''):
            values = input_data.split()
            for value in values:
                try:
                    fvalue = float(value)
                except (TypeError, ValueError) as exp:
                    raise_parse_error(node, 'Requires sequence of doubles')
            return input_data
        def gds_format_boolean(self, input_data, input_name=''):
            return '%s' % input_data
        def gds_validate_boolean(self, input_data, node, input_name=''):
            return input_data
        def gds_format_boolean_list(self, input_data, input_name=''):
            return '%s' % input_data
        def gds_validate_boolean_list(self, input_data, node, input_name=''):
            values = input_data.split()
            for value in values:
                if value not in ('true', '1', 'false', '0', ):
                    raise_parse_error(node, 'Requires sequence of booleans ("true", "1", "false", "0")')
            return input_data
        def gds_str_lower(self, instring):
            return instring.lower()
        def get_path_(self, node):
            path_list = []
            self.get_path_list_(node, path_list)
            path_list.reverse()
            path = '/'.join(path_list)
            return path
        Tag_strip_pattern_ = re_.compile(r'\{.*\}')
        def get_path_list_(self, node, path_list):
            if node is None:
                return
            tag = GeneratedsSuper.Tag_strip_pattern_.sub('', node.tag)
            if tag:
                path_list.append(tag)
            self.get_path_list_(node.getparent(), path_list)


#
# If you have installed IPython you can uncomment and use the following.
# IPython is available from http://ipython.scipy.org/.
#

## from IPython.Shell import IPShellEmbed
## args = ''
## ipshell = IPShellEmbed(args,
##     banner = 'Dropping into IPython',
##     exit_msg = 'Leaving Interpreter, back to program.')

# Then use the following line where and when you want to drop into the
# IPython shell:
#    ipshell('<some message> -- Entering ipshell.\nHit Ctrl-D to exit')

#
# Globals
#

ExternalEncoding = 'utf-8'
Tag_pattern_ = re_.compile(r'({.*})?(.*)')
STRING_CLEANUP_PAT = re_.compile(r"[\n\r\s]+")

#
# Support/utility functions.
#

def showIndent(outfile, level):
    for idx in range(level):
        outfile.write('    ')

def quote_xml(inStr):
    if not inStr:
        return ''
    s1 = (isinstance(inStr, str) and inStr or
          '%s' % inStr)
    s1 = s1.replace('&', '&amp;')
    s1 = s1.replace('<', '&lt;')
    s1 = s1.replace('>', '&gt;')
    return s1

def quote_attrib(inStr):
    s1 = (isinstance(inStr, str) and inStr or
          '%s' % inStr)
    s1 = s1.replace('&', '&amp;')
    s1 = s1.replace('<', '&lt;')
    s1 = s1.replace('>', '&gt;')
    if '"' in s1:
        if "'" in s1:
            s1 = '"%s"' % s1.replace('"', "&quot;")
        else:
            s1 = "'%s'" % s1
    else:
        s1 = '"%s"' % s1
    return s1

def quote_python(inStr):
    s1 = inStr
    if s1.find("'") == -1:
        if s1.find('\n') == -1:
            return "'%s'" % s1
        else:
            return "'''%s'''" % s1
    else:
        if s1.find('"') != -1:
            s1 = s1.replace('"', '\\"')
        if s1.find('\n') == -1:
            return '"%s"' % s1
        else:
            return '"""%s"""' % s1

def get_all_text_(node):
    if node.text is not None:
        text = node.text
    else:
        text = ''
    for child in node:
        if child.tail is not None:
            text += child.tail
    return text

def find_attr_value_(attr_name, node):
    attrs = node.attrib
    # First try with no namespace.
    value = attrs.get(attr_name)
    if value is None:
        # Now try the other possible namespaces.
        namespaces = node.nsmap.values()
        for namespace in namespaces:
            value = attrs.get('{%s}%s' % (namespace, attr_name, ))
            if value is not None:
                break
    return value


class GDSParseError(Exception):
    pass

def raise_parse_error(node, msg):
    if XMLParser_import_library == XMLParser_import_lxml:
        msg = '%s (element %s/line %d)' % (msg, node.tag, node.sourceline, )
    else:
        msg = '%s (element %s)' % (msg, node.tag, )
    raise GDSParseError(msg)


class MixedContainer:
    # Constants for category:
    CategoryNone = 0
    CategoryText = 1
    CategorySimple = 2
    CategoryComplex = 3
    # Constants for content_type:
    TypeNone = 0
    TypeText = 1
    TypeString = 2
    TypeInteger = 3
    TypeFloat = 4
    TypeDecimal = 5
    TypeDouble = 6
    TypeBoolean = 7
    def __init__(self, category, content_type, name, value):
        self.category = category
        self.content_type = content_type
        self.name = name
        self.value = value
    def getCategory(self):
        return self.category
    def getContenttype(self, content_type):
        return self.content_type
    def getValue(self):
        return self.value
    def getName(self):
        return self.name
    def export(self, outfile, level, name, namespace):
        if self.category == MixedContainer.CategoryText:
            # Prevent exporting empty content as empty lines.
            if self.value.strip():
                outfile.write(self.value)
        elif self.category == MixedContainer.CategorySimple:
            self.exportSimple(outfile, level, name)
        else:    # category == MixedContainer.CategoryComplex
            self.value.export(outfile, level, namespace,name)
    def exportSimple(self, outfile, level, name):
        if self.content_type == MixedContainer.TypeString:
            outfile.write('<%s>%s</%s>' % (self.name, self.value, self.name))
        elif self.content_type == MixedContainer.TypeInteger or \
                self.content_type == MixedContainer.TypeBoolean:
            outfile.write('<%s>%d</%s>' % (self.name, self.value, self.name))
        elif self.content_type == MixedContainer.TypeFloat or \
                self.content_type == MixedContainer.TypeDecimal:
            outfile.write('<%s>%f</%s>' % (self.name, self.value, self.name))
        elif self.content_type == MixedContainer.TypeDouble:
            outfile.write('<%s>%g</%s>' % (self.name, self.value, self.name))
    def exportLiteral(self, outfile, level, name):
        if self.category == MixedContainer.CategoryText:
            showIndent(outfile, level)
            outfile.write('model_.MixedContainer(%d, %d, "%s", "%s"),\n' % \
                (self.category, self.content_type, self.name, self.value))
        elif self.category == MixedContainer.CategorySimple:
            showIndent(outfile, level)
            outfile.write('model_.MixedContainer(%d, %d, "%s", "%s"),\n' % \
                (self.category, self.content_type, self.name, self.value))
        else:    # category == MixedContainer.CategoryComplex
            showIndent(outfile, level)
            outfile.write('model_.MixedContainer(%d, %d, "%s",\n' % \
                (self.category, self.content_type, self.name,))
            self.value.exportLiteral(outfile, level + 1)
            showIndent(outfile, level)
            outfile.write(')\n')


class MemberSpec_:
    def __init__(self, name='', data_type='', container=0):
        self.name = name
        self.data_type = data_type
        self.container = container
    def set_name(self, name): self.name = name
    def get_name(self): return self.name
    def set_data_type(self, data_type): self.data_type = data_type
    def get_data_type_chain(self): return self.data_type
    def get_data_type(self):
        if isinstance(self.data_type, list):
            if len(self.data_type) > 0:
                return self.data_type[-1]
            else:
                return 'xs:string'
        else:
            return self.data_type
    def set_container(self, container): self.container = container
    def get_container(self): return self.container

def _cast(typ, value):
    if typ is None or value is None:
        return value
    return typ(value)

#
# Data representation classes.
#

class orthoXML(GeneratedsSuper):
    """The OrthoXML root element. The source program/database of the file
    for instance OMA or InParanoid. The version number of the file.
    The version or release number of the source program/database at
    time the file was generated."""
    subclass = None
    superclass = None
    def __init__(self, origin=None, version=None, originVersion=None, notes=None, species=None, scores=None, groups=None, valueOf_=None):
        self.origin = _cast(None, origin)
        self.version = _cast(float, version)
        self.originVersion = _cast(None, originVersion)
        self.notes = notes
        if species is None:
            self.species = []
        else:
            self.species = species
        self.scores = scores
        self.groups = groups
    def factory(*args_, **kwargs_):
        if orthoXML.subclass:
            return orthoXML.subclass(*args_, **kwargs_)
        else:
            return orthoXML(*args_, **kwargs_)
    factory = staticmethod(factory)
    def get_notes(self): return self.notes
    def set_notes(self, notes): self.notes = notes
    def get_species(self): return self.species
    def set_species(self, species): self.species = species
    def add_species(self, value): self.species.append(value)
    def insert_species(self, index, value): self.species[index] = value
    def get_scores(self): return self.scores
    def set_scores(self, scores): self.scores = scores
    def get_groups(self): return self.groups
    def set_groups(self, groups): self.groups = groups
    def get_origin(self): return self.origin
    def set_origin(self, origin): self.origin = origin
    def get_version(self): return self.version
    def set_version(self, version): self.version = version
    def get_originVersion(self): return self.originVersion
    def set_originVersion(self, originVersion): self.originVersion = originVersion
    def export(self, outfile, level, namespace_='ortho:', name_='orthoXML', namespacedef_=''):
        showIndent(outfile, level)
        outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', ))
        already_processed = []
        self.exportAttributes(outfile, level, already_processed, namespace_, name_='orthoXML')
        if self.hasContent_():
            outfile.write('>\n')
            self.exportChildren(outfile, level + 1, namespace_, name_)
            showIndent(outfile, level)
            outfile.write('</%s%s>\n' % (namespace_, name_))
        else:
            outfile.write('/>\n')
    def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='orthoXML'):
        if self.origin is not None and 'origin' not in already_processed:
            already_processed.append('origin')
            outfile.write(' origin=%s' % (self.gds_format_string(quote_attrib(self.origin), input_name='origin'), ))
        if self.version is not None and 'version' not in already_processed:
            already_processed.append('version')
            outfile.write(' version="%s"' % self.gds_format_float(self.version, input_name='version'))
        if self.originVersion is not None and 'originVersion' not in already_processed:
            already_processed.append('originVersion')
            outfile.write(' originVersion=%s' % (self.gds_format_string(quote_attrib(self.originVersion), input_name='originVersion'), ))
    def exportChildren(self, outfile, level, namespace_='ortho:', name_='orthoXML', fromsubclass_=False):
        if self.notes:
            self.notes.export(outfile, level, namespace_, name_='notes')
        for species_ in self.species:
            species_.export(outfile, level, namespace_, name_='species')
        if self.scores:
            self.scores.export(outfile, level, namespace_, name_='scores')
        if self.groups:
            self.groups.export(outfile, level, namespace_, name_='groups', )
    def hasContent_(self):
        if (
            self.notes is not None or
            self.species or
            self.scores is not None or
            self.groups is not None
            ):
            return True
        else:
            return False
    def exportLiteral(self, outfile, level, name_='orthoXML'):
        level += 1
        self.exportLiteralAttributes(outfile, level, [], name_)
        if self.hasContent_():
            self.exportLiteralChildren(outfile, level, name_)
    def exportLiteralAttributes(self, outfile, level, already_processed, name_):
        if self.origin is not None and 'origin' not in already_processed:
            already_processed.append('origin')
            showIndent(outfile, level)
            outfile.write('origin = "%s",\n' % (self.origin,))
        if self.version is not None and 'version' not in already_processed:
            already_processed.append('version')
            showIndent(outfile, level)
            outfile.write('version = %f,\n' % (self.version,))
        if self.originVersion is not None and 'originVersion' not in already_processed:
            already_processed.append('originVersion')
            showIndent(outfile, level)
            outfile.write('originVersion = "%s",\n' % (self.originVersion,))
    def exportLiteralChildren(self, outfile, level, name_):
        if self.notes is not None:
            showIndent(outfile, level)
            outfile.write('notes=model_.notes(\n')
            self.notes.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
        showIndent(outfile, level)
        outfile.write('species=[\n')
        level += 1
        for species_ in self.species:
            showIndent(outfile, level)
            outfile.write('model_.species(\n')
            species_.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
        level -= 1
        showIndent(outfile, level)
        outfile.write('],\n')
        if self.scores is not None:
            showIndent(outfile, level)
            outfile.write('scores=model_.scores(\n')
            self.scores.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
        if self.groups is not None:
            showIndent(outfile, level)
            outfile.write('groups=model_.groups(\n')
            self.groups.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
    def build(self, node):
        self.buildAttributes(node, node.attrib, [])
        for child in node:
            nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
            self.buildChildren(child, node, nodeName_)
    def buildAttributes(self, node, attrs, already_processed):
        value = find_attr_value_('origin', node)
        if value is not None and 'origin' not in already_processed:
            already_processed.append('origin')
            self.origin = value
        value = find_attr_value_('version', node)
        if value is not None and 'version' not in already_processed:
            already_processed.append('version')
            try:
                self.version = float(value)
            except ValueError as exp:
                raise ValueError('Bad float/double attribute (version): %s' % exp)
        value = find_attr_value_('originVersion', node)
        if value is not None and 'originVersion' not in already_processed:
            already_processed.append('originVersion')
            self.originVersion = value
            self.originVersion = ' '.join(self.originVersion.split())
    def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
        if nodeName_ == 'notes':
            obj_ = notes.factory()
            obj_.build(child_)
            self.set_notes(obj_)
        elif nodeName_ == 'species':
            obj_ = species.factory()
            obj_.build(child_)
            self.species.append(obj_)
        elif nodeName_ == 'scores':
            obj_ = scores.factory()
            obj_.build(child_)
            self.set_scores(obj_)
        elif nodeName_ == 'groups':
            obj_ = groups.factory()
            obj_.build(child_)
            self.set_groups(obj_)
# end class orthoXML


class species(GeneratedsSuper):
    """The species element contains all sequences of one species. The NCBI
    Taxonomy identifier of the species to identify it unambiguously.
    The name of the species."""
    subclass = None
    superclass = None
    def __init__(self, name=None, NCBITaxId=None, database=None, notes=None, valueOf_=None):
        self.name = _cast(None, name)
        self.NCBITaxId = _cast(int, NCBITaxId)
        if database is None:
            self.database = []
        else:
            self.database = database
        self.notes = notes
    def factory(*args_, **kwargs_):
        if species.subclass:
            return species.subclass(*args_, **kwargs_)
        else:
            return species(*args_, **kwargs_)
    factory = staticmethod(factory)
    def get_database(self): return self.database
    def set_database(self, database): self.database = database
    def add_database(self, value): self.database.append(value)
    def insert_database(self, index, value): self.database[index] = value
    def get_notes(self): return self.notes
    def set_notes(self, notes): self.notes = notes
    def get_name(self): return self.name
    def set_name(self, name): self.name = name
    def get_NCBITaxId(self): return self.NCBITaxId
    def set_NCBITaxId(self, NCBITaxId): self.NCBITaxId = NCBITaxId
    def export(self, outfile, level, namespace_='ortho:', name_='species', namespacedef_=''):
        showIndent(outfile, level)
        outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', ))
        already_processed = []
        self.exportAttributes(outfile, level, already_processed, namespace_, name_='species')
        if self.hasContent_():
            outfile.write('>\n')
            self.exportChildren(outfile, level + 1, namespace_, name_)
            showIndent(outfile, level)
            outfile.write('</%s%s>\n' % (namespace_, name_))
        else:
            outfile.write('/>\n')
    def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='species'):
        if self.name is not None and 'name' not in already_processed:
            already_processed.append('name')
            outfile.write(' name=%s' % (self.gds_format_string(quote_attrib(self.name), input_name='name'), ))
        if self.NCBITaxId is not None and 'NCBITaxId' not in already_processed:
            already_processed.append('NCBITaxId')
            outfile.write(' NCBITaxId="%s"' % self.gds_format_integer(self.NCBITaxId, input_name='NCBITaxId'))
    def exportChildren(self, outfile, level, namespace_='ortho:', name_='species', fromsubclass_=False):
        for database_ in self.database:
            database_.export(outfile, level, namespace_, name_='database')
        if self.notes:
            self.notes.export(outfile, level, namespace_, name_='notes')
    def hasContent_(self):
        if (
            self.database or
            self.notes is not None
            ):
            return True
        else:
            return False
    def exportLiteral(self, outfile, level, name_='species'):
        level += 1
        self.exportLiteralAttributes(outfile, level, [], name_)
        if self.hasContent_():
            self.exportLiteralChildren(outfile, level, name_)
    def exportLiteralAttributes(self, outfile, level, already_processed, name_):
        if self.name is not None and 'name' not in already_processed:
            already_processed.append('name')
            showIndent(outfile, level)
            outfile.write('name = "%s",\n' % (self.name,))
        if self.NCBITaxId is not None and 'NCBITaxId' not in already_processed:
            already_processed.append('NCBITaxId')
            showIndent(outfile, level)
            outfile.write('NCBITaxId = %d,\n' % (self.NCBITaxId,))
    def exportLiteralChildren(self, outfile, level, name_):
        showIndent(outfile, level)
        outfile.write('database=[\n')
        level += 1
        for database_ in self.database:
            showIndent(outfile, level)
            outfile.write('model_.database(\n')
            database_.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
        level -= 1
        showIndent(outfile, level)
        outfile.write('],\n')
        if self.notes is not None:
            showIndent(outfile, level)
            outfile.write('notes=model_.notes(\n')
            self.notes.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
    def build(self, node):
        self.buildAttributes(node, node.attrib, [])
        for child in node:
            nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
            self.buildChildren(child, node, nodeName_)
    def buildAttributes(self, node, attrs, already_processed):
        value = find_attr_value_('name', node)
        if value is not None and 'name' not in already_processed:
            already_processed.append('name')
            self.name = value
        value = find_attr_value_('NCBITaxId', node)
        if value is not None and 'NCBITaxId' not in already_processed:
            already_processed.append('NCBITaxId')
            try:
                self.NCBITaxId = int(value)
            except ValueError as exp:
                raise_parse_error(node, 'Bad integer attribute: %s' % exp)
    def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
        if nodeName_ == 'database':
            obj_ = database.factory()
            obj_.build(child_)
            self.database.append(obj_)
        elif nodeName_ == 'notes':
            obj_ = notes.factory()
            obj_.build(child_)
            self.set_notes(obj_)
# end class species


class database(GeneratedsSuper):
    """A database element contains all genes from a single database/source.
    A Uniform Resource Identifier (URI) pointing to the gene. In the
    simplest case one could imagine a URL which in concatenation
    with the gene identifier links to the website of the gene in the
    source database. However, how this is used depends on the source
    of the orthoXML file. Name of the database. A Uniform Resource
    Identifier (URI) pointing to the protein. A Uniform Resource
    Identifier (URI) pointing to the transcript. Version number of
    the database."""
    subclass = None
    superclass = None
    def __init__(self, transcriptLink=None, protLink=None, geneLink=None, name=None, version=None, genes=None, valueOf_=None):
        self.transcriptLink = _cast(None, transcriptLink)
        self.protLink = _cast(None, protLink)
        self.geneLink = _cast(None, geneLink)
        self.name = _cast(None, name)
        self.version = _cast(None, version)
        self.genes = genes
    def factory(*args_, **kwargs_):
        if database.subclass:
            return database.subclass(*args_, **kwargs_)
        else:
            return database(*args_, **kwargs_)
    factory = staticmethod(factory)
    def get_genes(self): return self.genes
    def set_genes(self, genes): self.genes = genes
    def get_transcriptLink(self): return self.transcriptLink
    def set_transcriptLink(self, transcriptLink): self.transcriptLink = transcriptLink
    def get_protLink(self): return self.protLink
    def set_protLink(self, protLink): self.protLink = protLink
    def get_geneLink(self): return self.geneLink
    def set_geneLink(self, geneLink): self.geneLink = geneLink
    def get_name(self): return self.name
    def set_name(self, name): self.name = name
    def get_version(self): return self.version
    def set_version(self, version): self.version = version
    def export(self, outfile, level, namespace_='ortho:', name_='database', namespacedef_=''):
        showIndent(outfile, level)
        outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', ))
        already_processed = []
        self.exportAttributes(outfile, level, already_processed, namespace_, name_='database')
        if self.hasContent_():
            outfile.write('>\n')
            self.exportChildren(outfile, level + 1, namespace_, name_)
            showIndent(outfile, level)
            outfile.write('</%s%s>\n' % (namespace_, name_))
        else:
            outfile.write('/>\n')
    def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='database'):
        if self.transcriptLink is not None and 'transcriptLink' not in already_processed:
            already_processed.append('transcriptLink')
            outfile.write(' transcriptLink=%s' % (self.gds_format_string(quote_attrib(self.transcriptLink), input_name='transcriptLink'), ))
        if self.protLink is not None and 'protLink' not in already_processed:
            already_processed.append('protLink')
            outfile.write(' protLink=%s' % (self.gds_format_string(quote_attrib(self.protLink), input_name='protLink'), ))
        if self.geneLink is not None and 'geneLink' not in already_processed:
            already_processed.append('geneLink')
            outfile.write(' geneLink=%s' % (self.gds_format_string(quote_attrib(self.geneLink), input_name='geneLink'), ))
        if self.name is not None and 'name' not in already_processed:
            already_processed.append('name')
            outfile.write(' name=%s' % (self.gds_format_string(quote_attrib(self.name), input_name='name'), ))
        if self.version is not None and 'version' not in already_processed:
            already_processed.append('version')
            outfile.write(' version=%s' % (self.gds_format_string(quote_attrib(self.version), input_name='version'), ))
    def exportChildren(self, outfile, level, namespace_='ortho:', name_='database', fromsubclass_=False):
        if self.genes:
            self.genes.export(outfile, level, namespace_, name_='genes', )
    def hasContent_(self):
        if (
            self.genes is not None
            ):
            return True
        else:
            return False
    def exportLiteral(self, outfile, level, name_='database'):
        level += 1
        self.exportLiteralAttributes(outfile, level, [], name_)
        if self.hasContent_():
            self.exportLiteralChildren(outfile, level, name_)
    def exportLiteralAttributes(self, outfile, level, already_processed, name_):
        if self.transcriptLink is not None and 'transcriptLink' not in already_processed:
            already_processed.append('transcriptLink')
            showIndent(outfile, level)
            outfile.write('transcriptLink = "%s",\n' % (self.transcriptLink,))
        if self.protLink is not None and 'protLink' not in already_processed:
            already_processed.append('protLink')
            showIndent(outfile, level)
            outfile.write('protLink = "%s",\n' % (self.protLink,))
        if self.geneLink is not None and 'geneLink' not in already_processed:
            already_processed.append('geneLink')
            showIndent(outfile, level)
            outfile.write('geneLink = "%s",\n' % (self.geneLink,))
        if self.name is not None and 'name' not in already_processed:
            already_processed.append('name')
            showIndent(outfile, level)
            outfile.write('name = "%s",\n' % (self.name,))
        if self.version is not None and 'version' not in already_processed:
            already_processed.append('version')
            showIndent(outfile, level)
            outfile.write('version = "%s",\n' % (self.version,))
    def exportLiteralChildren(self, outfile, level, name_):
        if self.genes is not None:
            showIndent(outfile, level)
            outfile.write('genes=model_.genes(\n')
            self.genes.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
    def build(self, node):
        self.buildAttributes(node, node.attrib, [])
        for child in node:
            nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
            self.buildChildren(child, node, nodeName_)
    def buildAttributes(self, node, attrs, already_processed):
        value = find_attr_value_('transcriptLink', node)
        if value is not None and 'transcriptLink' not in already_processed:
            already_processed.append('transcriptLink')
            self.transcriptLink = value
        value = find_attr_value_('protLink', node)
        if value is not None and 'protLink' not in already_processed:
            already_processed.append('protLink')
            self.protLink = value
        value = find_attr_value_('geneLink', node)
        if value is not None and 'geneLink' not in already_processed:
            already_processed.append('geneLink')
            self.geneLink = value
        value = find_attr_value_('name', node)
        if value is not None and 'name' not in already_processed:
            already_processed.append('name')
            self.name = value
        value = find_attr_value_('version', node)
        if value is not None and 'version' not in already_processed:
            already_processed.append('version')
            self.version = value
    def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
        if nodeName_ == 'genes':
            obj_ = genes.factory()
            obj_.build(child_)
            self.set_genes(obj_)
# end class database


class genes(GeneratedsSuper):
    """A gene element represents a list of genes."""
    subclass = None
    superclass = None
    def __init__(self, gene=None, valueOf_=None):
        if gene is None:
            self.gene = []
        else:
            self.gene = gene
    def factory(*args_, **kwargs_):
        if genes.subclass:
            return genes.subclass(*args_, **kwargs_)
        else:
            return genes(*args_, **kwargs_)
    factory = staticmethod(factory)
    def get_gene(self): return self.gene
    def set_gene(self, gene): self.gene = gene
    def add_gene(self, value): self.gene.append(value)
    def insert_gene(self, index, value): self.gene[index] = value
    def export(self, outfile, level, namespace_='ortho:', name_='genes', namespacedef_=''):
        showIndent(outfile, level)
        outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', ))
        already_processed = []
        self.exportAttributes(outfile, level, already_processed, namespace_, name_='genes')
        if self.hasContent_():
            outfile.write('>\n')
            self.exportChildren(outfile, level + 1, namespace_, name_)
            showIndent(outfile, level)
            outfile.write('</%s%s>\n' % (namespace_, name_))
        else:
            outfile.write('/>\n')
    def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='genes'):
        pass
    def exportChildren(self, outfile, level, namespace_='ortho:', name_='genes', fromsubclass_=False):
        for gene_ in self.gene:
            gene_.export(outfile, level, namespace_, name_='gene')
    def hasContent_(self):
        if (
            self.gene
            ):
            return True
        else:
            return False
    def exportLiteral(self, outfile, level, name_='genes'):
        level += 1
        self.exportLiteralAttributes(outfile, level, [], name_)
        if self.hasContent_():
            self.exportLiteralChildren(outfile, level, name_)
    def exportLiteralAttributes(self, outfile, level, already_processed, name_):
        pass
    def exportLiteralChildren(self, outfile, level, name_):
        showIndent(outfile, level)
        outfile.write('gene=[\n')
        level += 1
        for gene_ in self.gene:
            showIndent(outfile, level)
            outfile.write('model_.gene(\n')
            gene_.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
        level -= 1
        showIndent(outfile, level)
        outfile.write('],\n')
    def build(self, node):
        self.buildAttributes(node, node.attrib, [])
        for child in node:
            nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
            self.buildChildren(child, node, nodeName_)
    def buildAttributes(self, node, attrs, already_processed):
        pass
    def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
        if nodeName_ == 'gene':
            obj_ = gene.factory()
            obj_.build(child_)
            self.gene.append(obj_)
# end class genes


class gene(GeneratedsSuper):
    """The gene element represents a single gene, protein or transcript. It
    is in fact a set of identifiers: one internal identifier that is
    used to link from geneRef elements in ortholog clusters and gene
    identifiers, transcript identifiers and protein identifiers to
    identify the molecule. The proper term for this element would
    therefore rather be molecule. However, as the general purpose of
    orthoXML is to represent orthology data for genes the term gene
    is used instead. Gene, protein and transcipt identifiers are
    optional but at least one of the three should be given. The
    source database of the gene is defined through the database
    element in which the gene element lies and the identifiers
    should stem from this source. Identifier of the gene in the
    source database. Multiple splice forms are possible by having
    the same geneId more than once. Internal identifier to link to
    the gene via the geneRef elements. Identifier of the protein in
    the source database. Identifier of the transcript in the source
    database."""
    subclass = None
    superclass = None
    def __init__(self, protId=None, id=None, geneId=None, transcriptId=None, valueOf_=None):
        self.protId = _cast(None, protId)
        self.id = _cast(int, id)
        self.geneId = _cast(None, geneId)
        self.transcriptId = _cast(None, transcriptId)
        pass
    def factory(*args_, **kwargs_):
        if gene.subclass:
            return gene.subclass(*args_, **kwargs_)
        else:
            return gene(*args_, **kwargs_)
    factory = staticmethod(factory)
    def get_protId(self): return self.protId
    def set_protId(self, protId): self.protId = protId
    def get_id(self): return self.id
    def set_id(self, id): self.id = id
    def get_geneId(self): return self.geneId
    def set_geneId(self, geneId): self.geneId = geneId
    def get_transcriptId(self): return self.transcriptId
    def set_transcriptId(self, transcriptId): self.transcriptId = transcriptId
    def export(self, outfile, level, namespace_='ortho:', name_='gene', namespacedef_=''):
        showIndent(outfile, level)
        outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', ))
        already_processed = []
        self.exportAttributes(outfile, level, already_processed, namespace_, name_='gene')
        if self.hasContent_():
            outfile.write('>\n')
            self.exportChildren(outfile, level + 1, namespace_, name_)
            outfile.write('</%s%s>\n' % (namespace_, name_))
        else:
            outfile.write('/>\n')
    def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='gene'):
        if self.protId is not None and 'protId' not in already_processed:
            already_processed.append('protId')
            outfile.write(' protId=%s' % (self.gds_format_string(quote_attrib(self.protId), input_name='protId'), ))
        if self.id is not None and 'id' not in already_processed:
            already_processed.append('id')
            outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id'))
        if self.geneId is not None and 'geneId' not in already_processed:
            already_processed.append('geneId')
            outfile.write(' geneId=%s' % (self.gds_format_string(quote_attrib(self.geneId), input_name='geneId'), ))
        if self.transcriptId is not None and 'transcriptId' not in already_processed:
            already_processed.append('transcriptId')
            outfile.write(' transcriptId=%s' % (self.gds_format_string(quote_attrib(self.transcriptId), input_name='transcriptId'), ))
    def exportChildren(self, outfile, level, namespace_='ortho:', name_='gene', fromsubclass_=False):
        pass
    def hasContent_(self):
        if (

            ):
            return True
        else:
            return False
    def exportLiteral(self, outfile, level, name_='gene'):
        level += 1
        self.exportLiteralAttributes(outfile, level, [], name_)
        if self.hasContent_():
            self.exportLiteralChildren(outfile, level, name_)
    def exportLiteralAttributes(self, outfile, level, already_processed, name_):
        if self.protId is not None and 'protId' not in already_processed:
            already_processed.append('protId')
            showIndent(outfile, level)
            outfile.write('protId = "%s",\n' % (self.protId,))
        if self.id is not None and 'id' not in already_processed:
            already_processed.append('id')
            showIndent(outfile, level)
            outfile.write('id = %d,\n' % (self.id,))
        if self.geneId is not None and 'geneId' not in already_processed:
            already_processed.append('geneId')
            showIndent(outfile, level)
            outfile.write('geneId = "%s",\n' % (self.geneId,))
        if self.transcriptId is not None and 'transcriptId' not in already_processed:
            already_processed.append('transcriptId')
            showIndent(outfile, level)
            outfile.write('transcriptId = "%s",\n' % (self.transcriptId,))
    def exportLiteralChildren(self, outfile, level, name_):
        pass
    def build(self, node):
        self.buildAttributes(node, node.attrib, [])
        for child in node:
            nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
            self.buildChildren(child, node, nodeName_)
    def buildAttributes(self, node, attrs, already_processed):
        value = find_attr_value_('protId', node)
        if value is not None and 'protId' not in already_processed:
            already_processed.append('protId')
            self.protId = value
        value = find_attr_value_('id', node)
        if value is not None and 'id' not in already_processed:
            already_processed.append('id')
            try:
                self.id = int(value)
            except ValueError as exp:
                raise_parse_error(node, 'Bad integer attribute: %s' % exp)
        value = find_attr_value_('geneId', node)
        if value is not None and 'geneId' not in already_processed:
            already_processed.append('geneId')
            self.geneId = value
        value = find_attr_value_('transcriptId', node)
        if value is not None and 'transcriptId' not in already_processed:
            already_processed.append('transcriptId')
            self.transcriptId = value
    def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
        pass
# end class gene


class scores(GeneratedsSuper):
    """A list of score definitions."""
    subclass = None
    superclass = None
    def __init__(self, scoreDef=None, valueOf_=None):
        if scoreDef is None:
            self.scoreDef = []
        else:
            self.scoreDef = scoreDef
    def factory(*args_, **kwargs_):
        if scores.subclass:
            return scores.subclass(*args_, **kwargs_)
        else:
            return scores(*args_, **kwargs_)
    factory = staticmethod(factory)
    def get_scoreDef(self): return self.scoreDef
    def set_scoreDef(self, scoreDef): self.scoreDef = scoreDef
    def add_scoreDef(self, value): self.scoreDef.append(value)
    def insert_scoreDef(self, index, value): self.scoreDef[index] = value
    def export(self, outfile, level, namespace_='ortho:', name_='scores', namespacedef_=''):
        showIndent(outfile, level)
        outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', ))
        already_processed = []
        self.exportAttributes(outfile, level, already_processed, namespace_, name_='scores')
        if self.hasContent_():
            outfile.write('>\n')
            self.exportChildren(outfile, level + 1, namespace_, name_)
            showIndent(outfile, level)
            outfile.write('</%s%s>\n' % (namespace_, name_))
        else:
            outfile.write('/>\n')
    def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='scores'):
        pass
    def exportChildren(self, outfile, level, namespace_='ortho:', name_='scores', fromsubclass_=False):
        for scoreDef_ in self.scoreDef:
            scoreDef_.export(outfile, level, namespace_, name_='scoreDef')
    def hasContent_(self):
        if (
            self.scoreDef
            ):
            return True
        else:
            return False
    def exportLiteral(self, outfile, level, name_='scores'):
        level += 1
        self.exportLiteralAttributes(outfile, level, [], name_)
        if self.hasContent_():
            self.exportLiteralChildren(outfile, level, name_)
    def exportLiteralAttributes(self, outfile, level, already_processed, name_):
        pass
    def exportLiteralChildren(self, outfile, level, name_):
        showIndent(outfile, level)
        outfile.write('scoreDef=[\n')
        level += 1
        for scoreDef_ in self.scoreDef:
            showIndent(outfile, level)
            outfile.write('model_.scoreDef(\n')
            scoreDef_.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
        level -= 1
        showIndent(outfile, level)
        outfile.write('],\n')
    def build(self, node):
        self.buildAttributes(node, node.attrib, [])
        for child in node:
            nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
            self.buildChildren(child, node, nodeName_)
    def buildAttributes(self, node, attrs, already_processed):
        pass
    def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
        if nodeName_ == 'scoreDef':
            obj_ = scoreDef.factory()
            obj_.build(child_)
            self.scoreDef.append(obj_)
# end class scores


class groups(GeneratedsSuper):
    """Represents the list of ortholog groups. Note that the purpose of
    OrthoXML is to store orthology assignment hence on the top level
    only ortholog groups are allowed."""
    subclass = None
    superclass = None
    def __init__(self, orthologGroup=None, valueOf_=None):
        if orthologGroup is None:
            self.orthologGroup = []
        else:
            self.orthologGroup = orthologGroup
    def factory(*args_, **kwargs_):
        if groups.subclass:
            return groups.subclass(*args_, **kwargs_)
        else:
            return groups(*args_, **kwargs_)
    factory = staticmethod(factory)
    def get_orthologGroup(self): return self.orthologGroup
    def set_orthologGroup(self, orthologGroup): self.orthologGroup = orthologGroup
    def add_orthologGroup(self, value): self.orthologGroup.append(value)
    def insert_orthologGroup(self, index, value): self.orthologGroup[index] = value
    def export(self, outfile, level, namespace_='ortho:', name_='groups', namespacedef_=''):
        showIndent(outfile, level)
        outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', ))
        already_processed = []
        self.exportAttributes(outfile, level, already_processed, namespace_, name_='groups')
        if self.hasContent_():
            outfile.write('>\n')
            self.exportChildren(outfile, level + 1, namespace_, name_)
            showIndent(outfile, level)
            outfile.write('</%s%s>\n' % (namespace_, name_))
        else:
            outfile.write('/>\n')
    def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='groups'):
        pass
    def exportChildren(self, outfile, level, namespace_='ortho:', name_='groups', fromsubclass_=False):
        for orthologGroup_ in self.orthologGroup:
            orthologGroup_.export(outfile, level, namespace_, name_='orthologGroup')
    def hasContent_(self):
        if (
            self.orthologGroup
            ):
            return True
        else:
            return False
    def exportLiteral(self, outfile, level, name_='groups'):
        level += 1
        self.exportLiteralAttributes(outfile, level, [], name_)
        if self.hasContent_():
            self.exportLiteralChildren(outfile, level, name_)
    def exportLiteralAttributes(self, outfile, level, already_processed, name_):
        pass
    def exportLiteralChildren(self, outfile, level, name_):
        showIndent(outfile, level)
        outfile.write('orthologGroup=[\n')
        level += 1
        for orthologGroup_ in self.orthologGroup:
            showIndent(outfile, level)
            outfile.write('model_.group(\n')
            orthologGroup_.exportLiteral(outfile, level, name_='group')
            showIndent(outfile, level)
            outfile.write('),\n')
        level -= 1
        showIndent(outfile, level)
        outfile.write('],\n')
    def build(self, node):
        self.buildAttributes(node, node.attrib, [])
        for child in node:
            nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
            self.buildChildren(child, node, nodeName_)
    def buildAttributes(self, node, attrs, already_processed):
        pass
    def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
        if nodeName_ == 'orthologGroup':
            obj_ = group.factory()
            obj_.build(child_)
            self.orthologGroup.append(obj_)
# end class groups


class group(GeneratedsSuper):
    """A group of genes or nested groups. In case of a orothologGroup
    element, all genes in the group or in the nested groups are
    orthologs to each other i.e. stem from the same gene in the last
    common ancester of the species. In case of a paralogGroup the
    genes are paralogs to each other. Subgroups within the group
    allow the represention of phylogenetic trees. For more details
    and examples see http://orthoxml.org/orthoxml_doc.html. A group
    can may contain two or more of the three alternatives geneRef,
    paralogGroup, and orthologGroup. By combining these, complex
    phylogenies are possible. Identifier for the group in context of
    the resource. This attribute is not required but if your
    resource provides identifiers for the ortholog groups we
    strongly recommend to use it at least for the top level groups."""
    subclass = None
    superclass = None
    def __init__(self, id=None, score=None, property=None, geneRef=None, paralogGroup=None, orthologGroup=None, notes=None, valueOf_=None):
        self.id = _cast(None, id)
        if score is None:
            self.score = []
        else:
            self.score = score
        if property is None:
            self.property = []
        else:
            self.property = property
        if geneRef is None:
            self.geneRef = []
        else:
            self.geneRef = geneRef
        if paralogGroup is None:
            self.paralogGroup = []
        else:
            self.paralogGroup = paralogGroup
        if orthologGroup is None:
            self.orthologGroup = []
        else:
            self.orthologGroup = orthologGroup
        self.notes = notes
    def factory(*args_, **kwargs_):
        if group.subclass:
            return group.subclass(*args_, **kwargs_)
        else:
            return group(*args_, **kwargs_)
    factory = staticmethod(factory)
    def get_score(self): return self.score
    def set_score(self, score): self.score = score
    def add_score(self, value): self.score.append(value)
    def insert_score(self, index, value): self.score[index] = value
    def get_property(self): return self.property
    def set_property(self, property): self.property = property
    def add_property(self, value): self.property.append(value)
    def insert_property(self, index, value): self.property[index] = value
    def get_geneRef(self): return self.geneRef
    def set_geneRef(self, geneRef): self.geneRef = geneRef
    def add_geneRef(self, value): self.geneRef.append(value)
    def insert_geneRef(self, index, value): self.geneRef[index] = value
    def get_paralogGroup(self): return self.paralogGroup
    def set_paralogGroup(self, paralogGroup): self.paralogGroup = paralogGroup
    def add_paralogGroup(self, value): self.paralogGroup.append(value)
    def insert_paralogGroup(self, index, value): self.paralogGroup[index] = value
    def get_orthologGroup(self): return self.orthologGroup
    def set_orthologGroup(self, orthologGroup): self.orthologGroup = orthologGroup
    def add_orthologGroup(self, value): self.orthologGroup.append(value)
    def insert_orthologGroup(self, index, value): self.orthologGroup[index] = value
    def get_notes(self): return self.notes
    def set_notes(self, notes): self.notes = notes
    def get_id(self): return self.id
    def set_id(self, id): self.id = id
    def export(self, outfile, level, namespace_='ortho:', name_='group', namespacedef_=''):
        showIndent(outfile, level)
        outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', ))
        already_processed = []
        self.exportAttributes(outfile, level, already_processed, namespace_, name_='group')
        if self.hasContent_():
            outfile.write('>\n')
            self.exportChildren(outfile, level + 1, namespace_, name_)
            showIndent(outfile, level)
            outfile.write('</%s%s>\n' % (namespace_, name_))
        else:
            outfile.write('/>\n')
    def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='group'):
        if self.id is not None and 'id' not in already_processed:
            already_processed.append('id')
            outfile.write(' id=%s' % (self.gds_format_string(quote_attrib(self.id), input_name='id'), ))
    def exportChildren(self, outfile, level, namespace_='ortho:', name_='group', fromsubclass_=False):
        for score_ in self.score:
            score_.export(outfile, level, namespace_, name_='score')
        for property_ in self.property:
            property_.export(outfile, level, namespace_, name_='property')
        for geneRef_ in self.geneRef:
            geneRef_.export(outfile, level, namespace_, name_='geneRef')
        for paralogGroup_ in self.paralogGroup:
            paralogGroup_.export(outfile, level, namespace_, name_='paralogGroup')
        for orthologGroup_ in self.orthologGroup:
            orthologGroup_.export(outfile, level, namespace_, name_='orthologGroup')
        if self.notes:
            self.notes.export(outfile, level, namespace_, name_='notes')
    def hasContent_(self):
        if (
            self.score or
            self.property or
            self.geneRef or
            self.paralogGroup or
            self.orthologGroup or
            self.notes is not None
            ):
            return True
        else:
            return False
    def exportLiteral(self, outfile, level, name_='group'):
        level += 1
        self.exportLiteralAttributes(outfile, level, [], name_)
        if self.hasContent_():
            self.exportLiteralChildren(outfile, level, name_)
    def exportLiteralAttributes(self, outfile, level, already_processed, name_):
        if self.id is not None and 'id' not in already_processed:
            already_processed.append('id')
            showIndent(outfile, level)
            outfile.write('id = "%s",\n' % (self.id,))
    def exportLiteralChildren(self, outfile, level, name_):
        showIndent(outfile, level)
        outfile.write('score=[\n')
        level += 1
        for score_ in self.score:
            showIndent(outfile, level)
            outfile.write('model_.score(\n')
            score_.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
        level -= 1
        showIndent(outfile, level)
        outfile.write('],\n')
        showIndent(outfile, level)
        outfile.write('property=[\n')
        level += 1
        for property_ in self.property:
            showIndent(outfile, level)
            outfile.write('model_.property(\n')
            property_.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
        level -= 1
        showIndent(outfile, level)
        outfile.write('],\n')
        showIndent(outfile, level)
        outfile.write('geneRef=[\n')
        level += 1
        for geneRef_ in self.geneRef:
            showIndent(outfile, level)
            outfile.write('model_.geneRef(\n')
            geneRef_.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
        level -= 1
        showIndent(outfile, level)
        outfile.write('],\n')
        showIndent(outfile, level)
        outfile.write('paralogGroup=[\n')
        level += 1
        for paralogGroup_ in self.paralogGroup:
            showIndent(outfile, level)
            outfile.write('model_.group(\n')
            paralogGroup_.exportLiteral(outfile, level, name_='group')
            showIndent(outfile, level)
            outfile.write('),\n')
        level -= 1
        showIndent(outfile, level)
        outfile.write('],\n')
        showIndent(outfile, level)
        outfile.write('orthologGroup=[\n')
        level += 1
        for orthologGroup_ in self.orthologGroup:
            showIndent(outfile, level)
            outfile.write('model_.group(\n')
            orthologGroup_.exportLiteral(outfile, level, name_='group')
            showIndent(outfile, level)
            outfile.write('),\n')
        level -= 1
        showIndent(outfile, level)
        outfile.write('],\n')
        if self.notes is not None:
            showIndent(outfile, level)
            outfile.write('notes=model_.notes(\n')
            self.notes.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
    def build(self, node):
        self.buildAttributes(node, node.attrib, [])
        for child in node:
            nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
            self.buildChildren(child, node, nodeName_)
    def buildAttributes(self, node, attrs, already_processed):
        value = find_attr_value_('id', node)
        if value is not None and 'id' not in already_processed:
            already_processed.append('id')
            self.id = value
    def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
        if nodeName_ == 'score':
            obj_ = score.factory()
            obj_.build(child_)
            self.score.append(obj_)
        elif nodeName_ == 'property':
            obj_ = property.factory()
            obj_.build(child_)
            self.property.append(obj_)
        elif nodeName_ == 'geneRef':
            obj_ = geneRef.factory()
            obj_.build(child_)
            self.geneRef.append(obj_)
        elif nodeName_ == 'paralogGroup':
            obj_ = group.factory()
            obj_.build(child_)
            self.paralogGroup.append(obj_)
        elif nodeName_ == 'orthologGroup':
            obj_ = group.factory()
            obj_.build(child_)
            self.orthologGroup.append(obj_)
        elif nodeName_ == 'notes':
            obj_ = notes.factory()
            obj_.build(child_)
            self.set_notes(obj_)
# end class group


class geneRef(GeneratedsSuper):
    """The geneRef element is a link to the gene definition under the
    species element. It defines the members of an ortholog or
    paralog group. The same gene can be referenced muliple times.
    The geneRef element can have multiple score elements and a notes
    elements as children. The notes element can for instance be used
    for special, ortholog-database-specific information (with
    InParanoid, for example, we could use it to mark the seed
    orthologs). Internal identifier for a gene element defined under
    the species element."""
    subclass = None
    superclass = None
    def __init__(self, id=None, score=None, notes=None, valueOf_=None):
        self.id = _cast(int, id)
        if score is None:
            self.score = []
        else:
            self.score = score
        self.notes = notes
    def factory(*args_, **kwargs_):
        if geneRef.subclass:
            return geneRef.subclass(*args_, **kwargs_)
        else:
            return geneRef(*args_, **kwargs_)
    factory = staticmethod(factory)
    def get_score(self): return self.score
    def set_score(self, score): self.score = score
    def add_score(self, value): self.score.append(value)
    def insert_score(self, index, value): self.score[index] = value
    def get_notes(self): return self.notes
    def set_notes(self, notes): self.notes = notes
    def get_id(self): return self.id
    def set_id(self, id): self.id = id
    def export(self, outfile, level, namespace_='ortho:', name_='geneRef', namespacedef_=''):
        showIndent(outfile, level)
        outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', ))
        already_processed = []
        self.exportAttributes(outfile, level, already_processed, namespace_, name_='geneRef')
        if self.hasContent_():
            outfile.write('>\n')
            self.exportChildren(outfile, level + 1, namespace_, name_)
            showIndent(outfile, level)
            outfile.write('</%s%s>\n' % (namespace_, name_))
        else:
            outfile.write('/>\n')
    def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='geneRef'):
        if self.id is not None and 'id' not in already_processed:
            already_processed.append('id')
            outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id'))
    def exportChildren(self, outfile, level, namespace_='ortho:', name_='geneRef', fromsubclass_=False):
        for score_ in self.score:
            score_.export(outfile, level, namespace_, name_='score')
        if self.notes:
            self.notes.export(outfile, level, namespace_, name_='notes')
    def hasContent_(self):
        if (
            self.score or
            self.notes is not None
            ):
            return True
        else:
            return False
    def exportLiteral(self, outfile, level, name_='geneRef'):
        level += 1
        self.exportLiteralAttributes(outfile, level, [], name_)
        if self.hasContent_():
            self.exportLiteralChildren(outfile, level, name_)
    def exportLiteralAttributes(self, outfile, level, already_processed, name_):
        if self.id is not None and 'id' not in already_processed:
            already_processed.append('id')
            showIndent(outfile, level)
            outfile.write('id = %d,\n' % (self.id,))
    def exportLiteralChildren(self, outfile, level, name_):
        showIndent(outfile, level)
        outfile.write('score=[\n')
        level += 1
        for score_ in self.score:
            showIndent(outfile, level)
            outfile.write('model_.score(\n')
            score_.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
        level -= 1
        showIndent(outfile, level)
        outfile.write('],\n')
        if self.notes is not None:
            showIndent(outfile, level)
            outfile.write('notes=model_.notes(\n')
            self.notes.exportLiteral(outfile, level)
            showIndent(outfile, level)
            outfile.write('),\n')
    def build(self, node):
        self.buildAttributes(node, node.attrib, [])
        for child in node:
            nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
            self.buildChildren(child, node, nodeName_)
    def buildAttributes(self, node, attrs, already_processed):
        value = find_attr_value_('id', node)
        if value is not None and 'id' not in already_processed:
            already_processed.append('id')
            try:
                self.id = int(value)
            except ValueError as exp:
                raise_parse_error(node, 'Bad integer attribute: %s' % exp)
    def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
        if nodeName_ == 'score':
            obj_ = score.factory()
            obj_.build(child_)
            self.score.append(obj_)
        elif nodeName_ == 'notes':
            obj_ = notes.factory()
            obj_.build(child_)
            self.set_notes(obj_)
# end class geneRef


class scoreDef(GeneratedsSuper):
    """The scoreDef element defines a score. One of the concepts of
    orthoXML is to be as flexible as possible but still uniformly
    parsable. Part of this is to allow every ortholog resource to
    give their own types of scores for groups or group members,
    which is done using score elements. Score elements can be
    defined to apply to either groups or geneRefs. It is possible to
    define multiple scores. An internal identifier to link to the
    scoreDef from a score element. Description of the score."""
    subclass = None
    superclass = None
    def __init__(self, id=None, desc=None, valueOf_=None):
        self.id = _cast(None, id)
        self.desc = _cast(None, desc)
        pass
    def factory(*args_, **kwargs_):
        if scoreDef.subclass:
            return scoreDef.subclass(*args_, **kwargs_)
        else:
            return scoreDef(*args_, **kwargs_)
    factory = staticmethod(factory)
    def get_id(self): return self.id
    def set_id(self, id): self.id = id
    def get_desc(self): return self.desc
    def set_desc(self, desc): self.desc = desc
    def export(self, outfile, level, namespace_='ortho:', name_='scoreDef', namespacedef_=''):
        showIndent(outfile, level)
        outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', ))
        already_processed = []
        self.exportAttributes(outfile, level, already_processed, namespace_, name_='scoreDef')
        if self.hasContent_():
            outfile.write('>\n')
            self.exportChildren(outfile, level + 1, namespace_, name_)
            outfile.write('</%s%s>\n' % (namespace_, name_))
        else:
            outfile.write('/>\n')
    def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='scoreDef'):
        if self.id is not None and 'id' not in already_processed:
            already_processed.append('id')
            outfile.write(' id=%s' % (quote_attrib(self.id), ))
        if self.desc is not None and 'desc' not in already_processed:
            already_processed.append('desc')
            outfile.write(' desc=%s' % (self.gds_format_string(quote_attrib(self.desc), input_name='desc'), ))
    def exportChildren(self, outfile, level, namespace_='ortho:', name_='scoreDef', fromsubclass_=False):
        pass
    def hasContent_(self):
        if (

            ):
            return True
        else:
            return False
    def exportLiteral(self, outfile, level, name_='scoreDef'):
        level += 1
        self.exportLiteralAttributes(outfile, level, [], name_)
        if self.hasContent_():
            self.exportLiteralChildren(outfile, level, name_)
    def exportLiteralAttributes(self, outfile, level, already_processed, name_):
        if self.id is not None and 'id' not in already_processed:
            already_processed.append('id')
            showIndent(outfile, level)
            outfile.write('id = "%s",\n' % (self.id,))
        if self.desc is not None and 'desc' not in already_processed:
            already_processed.append('desc')
            showIndent(outfile, level)
            outfile.write('desc = "%s",\n' % (self.desc,))
    def exportLiteralChildren(self, outfile, level, name_):
        pass
    def build(self, node):
        self.buildAttributes(node, node.attrib, [])
        for child in node:
            nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
            self.buildChildren(child, node, nodeName_)
    def buildAttributes(self, node, attrs, already_processed):
        value = find_attr_value_('id', node)
        if value is not None and 'id' not in already_processed:
            already_processed.append('id')
            self.id = value
        value = find_attr_value_('desc', node)
        if value is not None and 'desc' not in already_processed:
            already_processed.append('desc')
            self.desc = value
    def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
        pass
# end class scoreDef


class score(GeneratedsSuper):
    """The score element gives the value of a score and links it to the
    scoreDef element, which defines the score. It can be child of a
    group or a geneRef element to allow scoring on different levels.
    An identifier linking to the scoreDef element, which defines the
    score. The actual value of the score. For instance a confidence
    score of a group member."""
    subclass = None
    superclass = None
    def __init__(self, id=None, value=None, valueOf_=None):
        self.id = _cast(None, id)
        self.value = _cast(float, value)
        pass
    def factory(*args_, **kwargs_):
        if score.subclass:
            return score.subclass(*args_, **kwargs_)
        else:
            return score(*args_, **kwargs_)
    factory = staticmethod(factory)
    def get_id(self): return self.id
    def set_id(self, id): self.id = id
    def get_value(self): return self.value
    def set_value(self, value): self.value = value
    def export(self, outfile, level, namespace_='ortho:', name_='score', namespacedef_=''):
        showIndent(outfile, level)
        outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', ))
        already_processed = []
        self.exportAttributes(outfile, level, already_processed, namespace_, name_='score')
        if self.hasContent_():
            outfile.write('>\n')
            self.exportChildren(outfile, level + 1, namespace_, name_)
            outfile.write('</%s%s>\n' % (namespace_, name_))
        else:
            outfile.write('/>\n')
    def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='score'):
        if self.id is not None and 'id' not in already_processed:
            already_processed.append('id')
            outfile.write(' id=%s' % (quote_attrib(self.id), ))
        if self.value is not None and 'value' not in already_processed:
            already_processed.append('value')
            outfile.write(' value="%s"' % self.gds_format_float(self.value, input_name='value'))
    def exportChildren(self, outfile, level, namespace_='ortho:', name_='score', fromsubclass_=False):
        pass
    def hasContent_(self):
        if (

            ):
            return True
        else:
            return False
    def exportLiteral(self, outfile, level, name_='score'):
        level += 1
        self.exportLiteralAttributes(outfile, level, [], name_)
        if self.hasContent_():
            self.exportLiteralChildren(outfile, level, name_)
    def exportLiteralAttributes(self, outfile, level, already_processed, name_):
        if self.id is not None and 'id' not in already_processed:
            already_processed.append('id')
            showIndent(outfile, level)
            outfile.write('id = "%s",\n' % (self.id,))
        if self.value is not None and 'value' not in already_processed:
            already_processed.append('value')
            showIndent(outfile, level)
            outfile.write('value = %f,\n' % (self.value,))
    def exportLiteralChildren(self, outfile, level, name_):
        pass
    def build(self, node):
        self.buildAttributes(node, node.attrib, [])
        for child in node:
            nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
            self.buildChildren(child, node, nodeName_)
    def buildAttributes(self, node, attrs, already_processed):
        value = find_attr_value_('id', node)
        if value is not None and 'id' not in already_processed:
            already_processed.append('id')
            self.id = value
        value = find_attr_value_('value', node)
        if value is not None and 'value' not in already_processed:
            already_processed.append('value')
            try:
                self.value = float(value)
            except ValueError as exp:
                raise ValueError('Bad float/double attribute (value): %s' % exp)
    def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
        pass
# end class score


class property(GeneratedsSuper):
    """Key-value pair for group annotations, for instance statistics about
    the group members. The key of the key-value annotation pair. The
    value of the key-value annotation pair. Optional to allow flag
    like annotations."""
    subclass = None
    superclass = None
    def __init__(self, name=None, value=None, valueOf_=None):
        self.name = _cast(None, name)
        self.value = _cast(None, value)
        pass
    def factory(*args_, **kwargs_):
        if property.subclass:
            return property.subclass(*args_, **kwargs_)
        else:
            return property(*args_, **kwargs_)
    factory = staticmethod(factory)
    def get_name(self): return self.name
    def set_name(self, name): self.name = name
    def get_value(self): return self.value
    def set_value(self, value): self.value = value
    def export(self, outfile, level, namespace_='ortho:', name_='property', namespacedef_=''):
        showIndent(outfile, level)
        outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', ))
        already_processed = []
        self.exportAttributes(outfile, level, already_processed, namespace_, name_='property')
        if self.hasContent_():
            outfile.write('>\n')
            self.exportChildren(outfile, level + 1, namespace_, name_)
            outfile.write('</%s%s>\n' % (namespace_, name_))
        else:
            outfile.write('/>\n')
    def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='property'):
        if self.name is not None and 'name' not in already_processed:
            already_processed.append('name')
            outfile.write(' name=%s' % (self.gds_format_string(quote_attrib(self.name), input_name='name'), ))
        if self.value is not None and 'value' not in already_processed:
            already_processed.append('value')
            outfile.write(' value=%s' % (self.gds_format_string(quote_attrib(self.value), input_name='value'), ))
    def exportChildren(self, outfile, level, namespace_='ortho:', name_='property', fromsubclass_=False):
        pass
    def hasContent_(self):
        if (

            ):
            return True
        else:
            return False
    def exportLiteral(self, outfile, level, name_='property'):
        level += 1
        self.exportLiteralAttributes(outfile, level, [], name_)
        if self.hasContent_():
            self.exportLiteralChildren(outfile, level, name_)
    def exportLiteralAttributes(self, outfile, level, already_processed, name_):
        if self.name is not None and 'name' not in already_processed:
            already_processed.append('name')
            showIndent(outfile, level)
            outfile.write('name = "%s",\n' % (self.name,))
        if self.value is not None and 'value' not in already_processed:
            already_processed.append('value')
            showIndent(outfile, level)
            outfile.write('value = "%s",\n' % (self.value,))
    def exportLiteralChildren(self, outfile, level, name_):
        pass
    def build(self, node):
        self.buildAttributes(node, node.attrib, [])
        for child in node:
            nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
            self.buildChildren(child, node, nodeName_)
    def buildAttributes(self, node, attrs, already_processed):
        value = find_attr_value_('name', node)
        if value is not None and 'name' not in already_processed:
            already_processed.append('name')
            self.name = value
        value = find_attr_value_('value', node)
        if value is not None and 'value' not in already_processed:
            already_processed.append('value')
            self.value = value
    def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
        pass
# end class property


class notes(GeneratedsSuper):
    """The notes element is a special element, which allows adding
    information that is not general enough to be part of the
    standard. I.e. something specific to a particular ortholog
    database or algorithm. Notes elements will not be validated, so
    any child elements are legal. Notes elements can be children of
    the root element orthoXML, the species element, the
    orthologGroup element, the paralogGroup element, or the geneRef
    element."""
    subclass = None
    superclass = None
    def __init__(self, valueOf_=None, mixedclass_=None, content_=None):
        self.valueOf_ = valueOf_
        if mixedclass_ is None:
            self.mixedclass_ = MixedContainer
        else:
            self.mixedclass_ = mixedclass_
        if content_ is None:
            self.content_ = []
        else:
            self.content_ = content_
        self.valueOf_ = valueOf_
    def factory(*args_, **kwargs_):
        if notes.subclass:
            return notes.subclass(*args_, **kwargs_)
        else:
            return notes(*args_, **kwargs_)
    factory = staticmethod(factory)
    def get_valueOf_(self): return self.valueOf_
    def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
    def export(self, outfile, level, namespace_='ortho:', name_='notes', namespacedef_=''):
        showIndent(outfile, level)
        outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', ))
        already_processed = []
        self.exportAttributes(outfile, level, already_processed, namespace_, name_='notes')
        outfile.write('>')
        self.exportChildren(outfile, level + 1, namespace_, name_)
        outfile.write('</%s%s>\n' % (namespace_, name_))
    def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='notes'):
        pass
    def exportChildren(self, outfile, level, namespace_='ortho:', name_='notes', fromsubclass_=False):
        pass
    def hasContent_(self):
        if (
            self.valueOf_
            ):
            return True
        else:
            return False
    def exportLiteral(self, outfile, level, name_='notes'):
        level += 1
        self.exportLiteralAttributes(outfile, level, [], name_)
        if self.hasContent_():
            self.exportLiteralChildren(outfile, level, name_)
        showIndent(outfile, level)
        outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,))
    def exportLiteralAttributes(self, outfile, level, already_processed, name_):
        pass
    def exportLiteralChildren(self, outfile, level, name_):
        pass
    def build(self, node):
        self.buildAttributes(node, node.attrib, [])
        self.valueOf_ = get_all_text_(node)
        if node.text is not None:
            obj_ = self.mixedclass_(MixedContainer.CategoryText,
                MixedContainer.TypeNone, '', node.text)
            self.content_.append(obj_)
        for child in node:
            nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
            self.buildChildren(child, node, nodeName_)
    def buildAttributes(self, node, attrs, already_processed):
        pass
    def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
        if not fromsubclass_ and child_.tail is not None:
            obj_ = self.mixedclass_(MixedContainer.CategoryText,
                MixedContainer.TypeNone, '', child_.tail)
            self.content_.append(obj_)
        pass
# end class notes


USAGE_TEXT = """
Usage: python <Parser>.py [ -s ] <in_xml_file>
"""

def usage():
    print(USAGE_TEXT)
    sys.exit(1)


def get_root_tag(node):
    tag = Tag_pattern_.match(node.tag).groups()[-1]
    rootClass = globals().get(tag)
    return tag, rootClass


def parse(inFileName):
    doc = parsexml_(inFileName)
    rootNode = doc.getroot()
    rootTag, rootClass = get_root_tag(rootNode)
    if rootClass is None:
        rootTag = 'orthoXML'
        rootClass = orthoXML
    rootObj = rootClass.factory()
    rootObj.build(rootNode)
    # Enable Python to collect the space used by the DOM.
    doc = None
##     sys.stdout.write('<?xml version="1.0" ?>\n')
##     rootObj.export(sys.stdout, 0, name_=rootTag,
##         namespacedef_='xmlns:ortho="http://orthoXML.org/2011/"')
    return rootObj


def parseString(inString):
    from StringIO import StringIO
    doc = parsexml_(StringIO(inString))
    rootNode = doc.getroot()
    rootTag, rootClass = get_root_tag(rootNode)
    if rootClass is None:
        rootTag = 'orthoXML'
        rootClass = orthoXML
    rootObj = rootClass.factory()
    rootObj.build(rootNode)
    # Enable Python to collect the space used by the DOM.
    doc = None
##     sys.stdout.write('<?xml version="1.0" ?>\n')
##     rootObj.export(sys.stdout, 0, name_="orthoXML",
##         namespacedef_='xmlns:ortho="http://orthoXML.org/2011/"')
    return rootObj


def parseLiteral(inFileName):
    doc = parsexml_(inFileName)
    rootNode = doc.getroot()
    rootTag, rootClass = get_root_tag(rootNode)
    if rootClass is None:
        rootTag = 'orthoXML'
        rootClass = orthoXML
    rootObj = rootClass.factory()
    rootObj.build(rootNode)
    # Enable Python to collect the space used by the DOM.
    doc = None
##     sys.stdout.write('#from orthoxml import *\n\n')
##     sys.stdout.write('import orthoxml as model_\n\n')
##     sys.stdout.write('rootObj = model_.rootTag(\n')
##     rootObj.exportLiteral(sys.stdout, 0, name_=rootTag)
##     sys.stdout.write(')\n')
    return rootObj


def main():
    args = sys.argv[1:]
    if len(args) == 1:
        parse(args[0])
    else:
        usage()


if __name__ == '__main__':
    #import pdb; pdb.set_trace()
    main()


__all__ = [
    "database",
    "gene",
    "geneRef",
    "genes",
    "group",
    "groups",
    "notes",
    "orthoXML",
    "property",
    "score",
    "scoreDef",
    "scores",
    "species"
    ]
